Real-time PCR quantification of arbuscular mycorrhizal fungi: does the use of nuclear or mitochondrial markers make a difference?
Identifieur interne : 000C18 ( Main/Exploration ); précédent : 000C17; suivant : 000C19Real-time PCR quantification of arbuscular mycorrhizal fungi: does the use of nuclear or mitochondrial markers make a difference?
Auteurs : Alena Vo Ková [République tchèque] ; Jan Jansa [République tchèque] ; David Püschel [République tchèque] ; Manuela Krüger [République tchèque] ; Tomáš Cajthaml [République tchèque] ; Miroslav Vosátka [République tchèque] ; Martina Janoušková [République tchèque]Source :
- Mycorrhiza [ 1432-1890 ] ; 2017.
Descripteurs français
- KwdFr :
- MESH :
- génétique : ADN fongique, ADN mitochondrial, Glomeromycota, Mycorhizes, Noyau de la cellule.
- microbiologie : Medicago truncatula, Racines de plante.
- Réaction de polymérisation en chaine en temps réel.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA, Fungal, DNA, Mitochondrial.
- genetics : Cell Nucleus, Glomeromycota, Mycorrhizae.
- microbiology : Medicago truncatula, Plant Roots.
- Real-Time Polymerase Chain Reaction.
Abstract
Root colonization by arbuscular mycorrhizal fungi (AMF) can be quantified by different approaches. We compared two approaches that enable discrimination of specific AMF taxa and are therefore emerging as alternative to most commonly performed microscopic quantification of AMF in roots: quantitative real-time PCR (qPCR) using markers in nuclear ribosomal DNA (nrDNA) and mitochondrial ribosomal DNA (mtDNA). In a greenhouse experiment, Medicago truncatula was inoculated with four isolates belonging to different AMF species (Rhizophagus irregularis, Claroideoglomus claroideum, Gigaspora margarita and Funneliformis mosseae). The AMF were quantified in the root samples by qPCR targeted to both markers, microscopy and contents of AMF-specific phospholipid fatty acids (PLFA). Copy numbers of nrDNA and mtDNA were closely related within all isolates; however, the slopes and intercepts of the linear relationships significantly differed among the isolates. Across all isolates, a large proportion of variance in nrDNA copy numbers was explained by root colonization intensity or contents of AMF-specific PLFA, while variance in mtDNA copy numbers was mainly explained by differences among AMF isolates. We propose that the encountered inter-isolate differences in the ratios of mtDNA and nrDNA copy numbers reflect different physiological states of the isolates. Our results suggest that nrDNA is a more suitable marker region than mtDNA for the quantification of multiple AMF taxa as its copy numbers are better related to fungal biomass across taxa than are copy numbers of mtDNA.
DOI: 10.1007/s00572-017-0777-9
PubMed: 28569349
Affiliations:
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Republic.</nlm:affiliation><country xml:lang="fr">République tchèque</country><wicri:regionArea>Institute of Experimental Botany, The Czech Academy of Sciences, Rozvojová 263, Prague, 165 02</wicri:regionArea><wicri:noRegion>165 02</wicri:noRegion></affiliation></author><author><name sortKey="Cajthaml, Tomas" sort="Cajthaml, Tomas" uniqKey="Cajthaml T" first="Tomáš" last="Cajthaml">Tomáš Cajthaml</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Microbiology, The Czech Academy of Sciences, Vídeňská 1083, Prague, 142 20, Czech Republic.</nlm:affiliation><country xml:lang="fr">République tchèque</country><wicri:regionArea>Institute of Microbiology, The Czech Academy of Sciences, Vídeňská 1083, Prague, 142 20</wicri:regionArea><wicri:noRegion>142 20</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Institute for Environmental Studies, Faculty of Science, Charles University, Benátská 2, Prague, 128 01, Czech Republic.</nlm:affiliation><country xml:lang="fr">République tchèque</country><wicri:regionArea>Institute for Environmental Studies, Faculty of Science, Charles University, Benátská 2, Prague, 128 01</wicri:regionArea><wicri:noRegion>128 01</wicri:noRegion></affiliation></author><author><name sortKey="Vosatka, Miroslav" sort="Vosatka, Miroslav" uniqKey="Vosatka M" first="Miroslav" last="Vosátka">Miroslav Vosátka</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Botany, The Czech Academy of Sciences, Zámek 1, Průhonice, 252 43, Czech Republic.</nlm:affiliation><country xml:lang="fr">République tchèque</country><wicri:regionArea>Institute of Botany, The Czech Academy of Sciences, Zámek 1, Průhonice, 252 43</wicri:regionArea><wicri:noRegion>252 43</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, Prague, 128 44, Czech Republic.</nlm:affiliation><country xml:lang="fr">République tchèque</country><wicri:regionArea>Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, Prague, 128 44</wicri:regionArea><wicri:noRegion>128 44</wicri:noRegion></affiliation></author><author><name sortKey="Janouskova, Martina" sort="Janouskova, Martina" uniqKey="Janouskova M" first="Martina" last="Janoušková">Martina Janoušková</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Botany, The Czech Academy of Sciences, Zámek 1, Průhonice, 252 43, Czech Republic.</nlm:affiliation><country xml:lang="fr">République tchèque</country><wicri:regionArea>Institute of Botany, The Czech Academy of Sciences, Zámek 1, Průhonice, 252 43</wicri:regionArea><wicri:noRegion>252 43</wicri:noRegion></affiliation></author></analytic><series><title level="j">Mycorrhiza</title><idno type="eISSN">1432-1890</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Cell Nucleus (genetics)</term><term>DNA, Fungal (genetics)</term><term>DNA, Mitochondrial (genetics)</term><term>Glomeromycota (genetics)</term><term>Medicago truncatula (microbiology)</term><term>Mycorrhizae (genetics)</term><term>Plant Roots (microbiology)</term><term>Real-Time Polymerase Chain Reaction (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN fongique (génétique)</term><term>ADN mitochondrial (génétique)</term><term>Glomeromycota (génétique)</term><term>Medicago truncatula (microbiologie)</term><term>Mycorhizes (génétique)</term><term>Noyau de la cellule (génétique)</term><term>Racines de plante (microbiologie)</term><term>Réaction de polymérisation en chaine en temps réel (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Fungal</term><term>DNA, Mitochondrial</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Cell Nucleus</term><term>Glomeromycota</term><term>Mycorrhizae</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN fongique</term><term>ADN mitochondrial</term><term>Glomeromycota</term><term>Mycorhizes</term><term>Noyau de la cellule</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Medicago truncatula</term><term>Racines de plante</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Medicago truncatula</term><term>Plant Roots</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Real-Time Polymerase Chain Reaction</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Réaction de polymérisation en chaine en temps réel</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Root colonization by arbuscular mycorrhizal fungi (AMF) can be quantified by different approaches. We compared two approaches that enable discrimination of specific AMF taxa and are therefore emerging as alternative to most commonly performed microscopic quantification of AMF in roots: quantitative real-time PCR (qPCR) using markers in nuclear ribosomal DNA (nrDNA) and mitochondrial ribosomal DNA (mtDNA). In a greenhouse experiment, Medicago truncatula was inoculated with four isolates belonging to different AMF species (Rhizophagus irregularis, Claroideoglomus claroideum, Gigaspora margarita and Funneliformis mosseae). The AMF were quantified in the root samples by qPCR targeted to both markers, microscopy and contents of AMF-specific phospholipid fatty acids (PLFA). Copy numbers of nrDNA and mtDNA were closely related within all isolates; however, the slopes and intercepts of the linear relationships significantly differed among the isolates. Across all isolates, a large proportion of variance in nrDNA copy numbers was explained by root colonization intensity or contents of AMF-specific PLFA, while variance in mtDNA copy numbers was mainly explained by differences among AMF isolates. We propose that the encountered inter-isolate differences in the ratios of mtDNA and nrDNA copy numbers reflect different physiological states of the isolates. Our results suggest that nrDNA is a more suitable marker region than mtDNA for the quantification of multiple AMF taxa as its copy numbers are better related to fungal biomass across taxa than are copy numbers of mtDNA.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">28569349</PMID><DateCompleted><Year>2018</Year><Month>01</Month><Day>10</Day></DateCompleted><DateRevised><Year>2018</Year><Month>12</Month><Day>02</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1432-1890</ISSN><JournalIssue CitedMedium="Internet"><Volume>27</Volume><Issue>6</Issue><PubDate><Year>2017</Year><Month>Aug</Month></PubDate></JournalIssue><Title>Mycorrhiza</Title><ISOAbbreviation>Mycorrhiza</ISOAbbreviation></Journal><ArticleTitle>Real-time PCR quantification of arbuscular mycorrhizal fungi: does the use of nuclear or mitochondrial markers make a difference?</ArticleTitle><Pagination><MedlinePgn>577-585</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s00572-017-0777-9</ELocationID><Abstract><AbstractText>Root colonization by arbuscular mycorrhizal fungi (AMF) can be quantified by different approaches. We compared two approaches that enable discrimination of specific AMF taxa and are therefore emerging as alternative to most commonly performed microscopic quantification of AMF in roots: quantitative real-time PCR (qPCR) using markers in nuclear ribosomal DNA (nrDNA) and mitochondrial ribosomal DNA (mtDNA). In a greenhouse experiment, Medicago truncatula was inoculated with four isolates belonging to different AMF species (Rhizophagus irregularis, Claroideoglomus claroideum, Gigaspora margarita and Funneliformis mosseae). The AMF were quantified in the root samples by qPCR targeted to both markers, microscopy and contents of AMF-specific phospholipid fatty acids (PLFA). Copy numbers of nrDNA and mtDNA were closely related within all isolates; however, the slopes and intercepts of the linear relationships significantly differed among the isolates. Across all isolates, a large proportion of variance in nrDNA copy numbers was explained by root colonization intensity or contents of AMF-specific PLFA, while variance in mtDNA copy numbers was mainly explained by differences among AMF isolates. We propose that the encountered inter-isolate differences in the ratios of mtDNA and nrDNA copy numbers reflect different physiological states of the isolates. Our results suggest that nrDNA is a more suitable marker region than mtDNA for the quantification of multiple AMF taxa as its copy numbers are better related to fungal biomass across taxa than are copy numbers of mtDNA.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Voříšková</LastName><ForeName>Alena</ForeName><Initials>A</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-2108-7892</Identifier><AffiliationInfo><Affiliation>Institute of Botany, The Czech Academy of Sciences, Zámek 1, Průhonice, 252 43, Czech Republic. alena.voriskova@ibot.cas.cz.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, Prague, 128 44, Czech Republic. alena.voriskova@ibot.cas.cz.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jansa</LastName><ForeName>Jan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Institute of Microbiology, The Czech Academy of Sciences, Vídeňská 1083, Prague, 142 20, Czech Republic.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Püschel</LastName><ForeName>David</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Institute of Botany, The Czech Academy of Sciences, Zámek 1, Průhonice, 252 43, Czech Republic.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institute of Microbiology, The Czech Academy of Sciences, Vídeňská 1083, Prague, 142 20, Czech Republic.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Krüger</LastName><ForeName>Manuela</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Institute of Botany, The Czech Academy of Sciences, Zámek 1, Průhonice, 252 43, Czech Republic.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institute of Experimental Botany, The Czech Academy of Sciences, Rozvojová 263, Prague, 165 02, Czech Republic.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cajthaml</LastName><ForeName>Tomáš</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Institute of Microbiology, The Czech Academy of Sciences, Vídeňská 1083, Prague, 142 20, Czech Republic.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institute for Environmental Studies, Faculty of Science, Charles University, Benátská 2, Prague, 128 01, Czech Republic.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vosátka</LastName><ForeName>Miroslav</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Institute of Botany, The Czech Academy of Sciences, Zámek 1, Průhonice, 252 43, Czech Republic.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, Prague, 128 44, Czech Republic.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Janoušková</LastName><ForeName>Martina</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Institute of Botany, The Czech Academy of Sciences, Zámek 1, Průhonice, 252 43, Czech Republic.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>05</Month><Day>31</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>Mycorrhiza</MedlineTA><NlmUniqueID>100955036</NlmUniqueID><ISSNLinking>0940-6360</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004271">DNA, Fungal</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004272">DNA, Mitochondrial</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D002467" MajorTopicYN="N">Cell Nucleus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004271" MajorTopicYN="N">DNA, Fungal</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004272" MajorTopicYN="N">DNA, Mitochondrial</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D055137" MajorTopicYN="N">Glomeromycota</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D046913" MajorTopicYN="N">Medicago truncatula</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D038821" MajorTopicYN="N">Mycorrhizae</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018517" MajorTopicYN="N">Plant Roots</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D060888" MajorTopicYN="Y">Real-Time Polymerase Chain Reaction</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Arbuscular mycorrhizal fungi</Keyword><Keyword MajorTopicYN="N">Isolate discrimination</Keyword><Keyword MajorTopicYN="N">Microsymbiont screening</Keyword><Keyword MajorTopicYN="N">Mitochondrial DNA</Keyword><Keyword MajorTopicYN="N">Molecular genetic quantification</Keyword><Keyword MajorTopicYN="N">Nuclear ribosomal DNA</Keyword><Keyword MajorTopicYN="N">PLFA</Keyword><Keyword 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